Additionally, mutations in TP53, CDH1, NCOR1, PTEN and NF1, CCND1 amplification, as well as loss of TP53 and KMT2C were associated (FDR q-value <0.1, permutation test) with ‘APOBEC high’ samples in different breast cancer subtypes (Fig. 1c), which could explain the heterogeneity in APOBEC3 enrichment among samples within subtypes. Here, PTEN is linked to breast cancer.